Faculty and Staff

High-resolution, global quantification of fossil fuel CO[subscript 2] emissions is emerging as a critical need in carbon cycle science and climate policy. We build upon a previously developed fossil fuel data assimilation system (FFDAS) for estimating global high-resolution fossil fuel CO[subscript 2] emissions. We have improved the underlying observationally based data sources, expanded the approach through treatment of separate emitting sectors including a new pointwise database of global power plants, and extended the results to cover a 1997 to 2010 time series at a spatial resolution of 0.1°. Long-term trend analysis of the resulting global emissions shows subnational spatial structure in large active economies such as the United States, China, and India. These three countries, in particular, show different long-term trends and exploration of the trends in nighttime lights, and population reveal a decoupling of population and emissions at the subnational level. Analysis of shorter-term variations reveals the impact of the 2008–2009 global financial crisis with widespread negative emission anomalies across the U.S. and Europe. We have used a center of mass (CM) calculation as a compact metric to express the time evolution of spatial patterns in fossil fuel CO[subscript 2] emissions. The global emission CM has moved toward the east and somewhat south between 1997 and 2010, driven by the increase in emissions in China and South Asia over this time period. Analysis at the level of individual countries reveals per capita CO[subscript 2] emission migration in both Russia and India. The per capita emission CM holds potential as a way to succinctly analyze subnational shifts in carbon intensity over time. Uncertainties are generally lower than the previous version of FFDAS due mainly to an improved nightlight data set.

The emergence of the disease chytridiomycosis caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd) has been implicated in dramatic global amphibian declines. Although many species have undergone catastrophic declines and/or extinctions, others appear to be unaffected or persist at reduced frequencies after Bd outbreaks. The reasons behind this variance in disease outcomes are poorly understood: differences in host immune responses have been proposed, yet previous studies suggest a lack of robust immune responses to Bd in susceptible species. Here, we sequenced transcriptomes from clutch-mates of a highly susceptible amphibian, Atelopus zeteki, with different infection histories. We found significant changes in expression of numerous genes involved in innate and inflammatory responses in infected frogs despite high susceptibility to chytridiomycosis.

We show evidence of acquired immune responses generated against Bd, including increased expression of immunoglobulins and major histocompatibility complex genes. In addition, fungal-killing genes had significantly greater expression in frogs previously exposed to Bd compared with Bd-naïve frogs, including chitinase and serine-type proteases. However, our results appear to confirm recent in vitro evidence of immune suppression by Bd, demonstrated by decreased expression of lymphocyte genes in the spleen of infected compared with control frogs. We propose susceptibility to chytridiomycosis is not due to lack of Bd-specific immune responses but instead is caused by failure of those responses to be effective. Ineffective immune pathway activation and timing of antibody production are discussed as potential mechanisms. However, in light of our findings, suppression of key immune responses by Bd is likely an important factor in the lethality of this fungus.

Large urban emissions of greenhouse gases result in large atmospheric enhancements relative to background that are easily measured. Using CO₂ mole fractions and Δ¹⁴C and δ¹³C values of CO₂ in the Los Angeles megacity observed in inland Pasadena (2006–2013) and coastal Palos Verdes peninsula (autumn 2009–2013), we have determined time series for CO₂ contributions from fossil fuel combustion (C_ff) for both sites and broken those down into contributions from petroleum and/or gasoline and natural gas burning for Pasadena. We find a 10 % reduction in Pasadena C_ff during the Great Recession of 2008–2010, which is consistent with the bottom-up inventory determined by the California Air Resources Board. The isotopic variations and total atmospheric CO₂ from our observations are used to infer seasonality of natural gas and petroleum combustion. The trend of CO₂ contributions to the atmosphere from natural gas combustion is out of phase with the seasonal cycle of total natural gas combustion seasonal patterns in bottom-up inventories but is consistent with the seasonality of natural gas usage by the area's electricity generating power plants. For petroleum, the inferred seasonality of CO₂ contributions from burning petroleum is delayed by several months relative to usage indicated by statewide gasoline taxes. Using the high-resolution Hestia-LA data product to compare C_ff from parts of the basin sampled by winds at different times of year, we find that variations in observed fossil fuel CO₂ reflect seasonal variations in wind direction. The seasonality of the local CO₂ excess from fossil fuel combustion along the coast, on Palos Verdes peninsula, is higher in autumn and winter than spring and summer, almost completely out of phase with that from Pasadena, also because of the annual variations of winds in the region. Variations in fossil fuel CO₂ signals are consistent with sampling the bottom-up Hestia-LA fossil CO₂ emissions product for sub-city source regions in the LA megacity domain when wind directions are considered.

Atmospheric CO₂ inversions estimate surface carbon fluxes from an optimal fit to atmospheric CO₂ measurements, usually including prior constraints on the flux estimates. Eleven sets of carbon flux estimates are compared, generated by different inversions systems that vary in their inversions methods, choice of atmospheric data, transport model and prior information. The inversions were run for at least 5 yr in the period between 1990 and 2010. Mean fluxes for 2001–2004, seasonal cycles, interannual variability and trends are compared for the tropics and northern and southern extra-tropics, and separately for land and ocean. Some continental/basin-scale subdivisions are also considered where the atmospheric network is denser. Four-year mean fluxes are reasonably consistent across inversions at global/latitudinal scale, with a large total (land plus ocean) carbon uptake in the north (−3.4 Pg C yr^-1 (±0.5 Pg C yr^-1 standard deviation), with slightly more uptake over land than over ocean), a significant although more variable source over the tropics (1.6 ± 0.9 Pg C yr^-1) and a compensatory sink of similar magnitude in the south (−1.4 ± 0.5 Pg C yr^-1) corresponding mainly to an ocean sink. Largest differences across inversions occur in the balance between tropical land sources and southern land sinks. Interannual variability (IAV) in carbon fluxes is larger for land than ocean regions (standard deviation around 1.06 versus 0.33 Pg C yr[superscript −1] for the 1996–2007 period), with much higher consistency among the inversions for the land. While the tropical land explains most of the IAV (standard deviation ~ 0.65 Pg C yr^-1), the northern and southern land also contribute (standard deviation ~ 0.39 Pg C yr^-1). Most inversions tend to indicate an increase of the northern land carbon uptake from late 1990s to 2008 (around 0.1 Pg C yr^-1, predominantly in North Asia. The mean seasonal cycle appears to be well constrained by the atmospheric data over the northern land (at the continental scale), but still highly dependent on the prior flux seasonality over the ocean. Finally we provide recommendations to interpret the regional fluxes, along with the uncertainty estimates.

This paper presents an analysis of methane emissions from the Los Angeles Basin at monthly timescales across a 4-year time period – from September 2011 to August 2015. Using observations acquired by a ground-based near-infrared remote sensing instrument on Mount Wilson, California, combined with atmospheric CH₄–CO₂ tracer–tracer correlations, we observed −18 to +22 % monthly variability in CH₄ : CO₂ from the annual mean in the Los Angeles Basin. Top-down estimates of methane emissions for the basin also exhibit significant monthly variability (−19 to +31 % from annual mean and a maximum month-to-month change of 47 %). During this period, methane emissions consistently peaked in the late summer/early fall and winter. The estimated annual methane emissions did not show a statistically significant trend over the 2011 to 2015 time period.

Amphibians vary in their response to infection by the amphibian-killing chytrid fungus, Batrachochytrium dendrobatidis (Bd). Highly susceptible species are the first to decline and/or disappear once Bd arrives at a site. These competent hosts likely facilitate Bd proliferation because of ineffective innate and/or acquired immune defenses. We show that Atelopus zeteki, a highly susceptible species that has undergone substantial population declines throughout its range, rapidly and exponentially increases skin Bd infection intensity, achieving intensities that are several orders of magnitude greater than most other species reported. We experimentally infected individuals that were never exposed to Bd (n = 5) or previously exposed to an attenuated Bd strain (JEL427-P39; n = 3). Within seven days post-inoculation, the average Bd infection intensity was 18,213 zoospores (SE: 9,010; range: 0 to 66,928).

Both average Bd infection intensity and zoospore output (i.e., the number of zoospores released per minute by an infected individual) increased exponentially until time of death (t₅₀ = 7.018, p<0.001, t₄₆ = 3.164, p = 0.001, respectively). Mean Bd infection intensity and zoospore output at death were 4,334,422 zoospores (SE: 1,236,431) and 23.55 zoospores per minute (SE: 22.78), respectively, with as many as 9,584,158 zoospores on a single individual. The daily percent increases in Bd infection intensity and zoospore output were 35.4% (SE: 0.05) and 13.1% (SE: 0.04), respectively. We also found that Bd infection intensity and zoospore output were positively correlated (t₄₃ = 3.926, p<0.001). All animals died between 22 and 33 days post-inoculation (mean: 28.88; SE: 1.58). Prior Bd infection had no effect on survival, Bd infection intensity, or zoospore output. We conclude that A. zeteki, a highly susceptible amphibian species, may be an acute supershedder. Our results can inform epidemiological models to estimate Bd outbreak probability, especially as they relate to reintroduction programs.

Laboratory investigations into the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), have accelerated recently, given the pathogen’s role in causing the global decline and extinction of amphibians. Studies in which host animals were exposed to Bd have largely assumed that lab-maintained pathogen cultures retained the infective and pathogenic properties of wild isolates. Attenuated pathogenicity is common in artificially maintained cultures of other pathogenic fungi, but to date, it is unknown whether, and to what degree, Bd might change in culture. We compared zoospore production over time in two samples of a single Bd isolate having different passage histories: one maintained in artificial media for more than six years (JEL427-P39), and one recently thawed from cryopreserved stock (JEL427-P9). In a common garden experiment, we then exposed two different amphibian species, Eleutherodactylus coqui and Atelopus zeteki, to both cultures to test whether Bd attenuates in pathogenicity with in vitro passages. The culture with the shorter passage history, JEL427-P9, had significantly greater zoospore densities over time compared to JEL427-P39. This difference in zoospore production was associated with a difference in pathogenicity for a susceptible amphibian species, indicating that fecundity may be an important virulence factor for Bd. In the 130-day experiment, Atelopus zeteki frogs exposed to the JEL427-P9 culture experienced higher average infection intensity and 100% mortality, compared with 60% mortality for frogs exposed to JEL427-P39. This effect was not observed with Eleutherodactylus coqui, which was able to clear infection. We hypothesize that the differences in phenotypic performance observed with Atelopus zeteki are rooted in changes of the Bd genome. Future investigations enabled by this study will focus on the underlying mechanisms of Bd pathogenicity.

Attributing observed CO2 variations to human or natural cause is critical to deducing and tracking emissions from observations. We have used in situ CO2, CO, and planetary boundary layer height (PBLH) measurements recorded during the CalNex-LA (CARB et al., 2008) ground campaign of 15 May-15 June 2010, in Pasadena, CA, to deduce the diurnally varying anthropogenic component of observed CO2 in the megacity of Los Angeles (LA). This affordable and simple technique, validated by carbon isotope observations and WRF-STILT (Weather Research and Forecasting model - Stochastic Time-Inverted Lagrangian Transport model) predictions, is shown to robustly attribute observed CO2 variation to anthropogenic or biogenic origin over the entire diurnal cycle. During CalNex-LA, local fossil fuel combustion contributed up to similar to 50% of the observed CO2 enhancement overnight, and similar to 100% of the enhancement near midday. This suggests that sufficiently accurate total column CO2 observations recorded near midday, such as those from the GOSAT or OCO-2 satellites, can potentially be used to track anthropogenic emissions from the LA megacity.

We present a high-resolution atmospheric inversion system combining a Lagrangian Particle Dispersion Model (LPDM) and the Weather Research and Forecasting model (WRF), and test the impact of assimilating meteorological observation on transport accuracy. A Four Dimensional Data Assimilation (FDDA) technique continuously assimilates meteorological observations from various observing systems into the transport modeling system, and is coupled to the high resolution CO₂ emission product Hestia to simulate the atmospheric mole fractions of CO₂. For the Indianapolis Flux Experiment (INFLUX) project, we evaluated the impact of assimilating different meteorological observation systems on the linearized adjoint solutions and the CO₂ inverse fluxes estimated using observed CO₂ mole fractions from 11 out of 12 communications towers over Indianapolis for the Sep.-Nov. 2013 period. While assimilating WMO surface measurements improved the simulated wind speed and direction, their impact on the planetary boundary layer (PBL) was limited. Simulated PBL wind statistics improved significantly when assimilating upper-air observations from the commercial airline program Aircraft Communications Addressing and Reporting System (ACARS) and continuous ground-based Doppler lidar wind observations. Wind direction mean absolute error (MAE) decreased from 26 to 14 degrees and the wind speed MAE decreased from 2.0 to 1.2 m s_-1, while the bias remains small in all configurations (< 6 degrees and 0.2 m s_-1). Wind speed MAE and ME are larger in daytime than in nighttime. PBL depth MAE is reduced by ~10%, with little bias reduction. The inverse results indicate that the spatial distribution of CO₂ inverse fluxes were affected by the model performance while the overall flux estimates changed little across WRF simulations when aggregated over the entire domain. Our results show that PBL wind observations are a potent tool for increasing the precision of urban meteorological reanalyses, but that the impact on inverse flux estimates is dependent on the specific urban environment.

The objective of the Indianapolis Flux Experiment (INFLUX) is to develop, evaluate and improve methods for measuring greenhouse gas (GHG) emissions from cities. INFLUX’s scientific objectives are to quantify CO₂ and CH₄ emission rates at 1 km₂ resolution with a 10% or better accuracy and precision, to determine whole-city emissions with similar skill, and to achieve high (weekly or finer) temporal resolution at both spatial resolutions. The experiment employs atmospheric GHG measurements from both towers and aircraft, atmospheric transport observations and models, and activity-based inventory products to quantify urban GHG emissions. Multiple, independent methods for estimating urban emissions are a central facet of our experimental design. INFLUX was initiated in 2010 and measurements and analyses are ongoing. To date we have quantified urban atmospheric GHG enhancements using aircraft and towers with measurements collected over multiple years, and have estimated whole-city CO₂ and CH₄ emissions using aircraft and tower GHG measurements, and inventory methods. Significant differences exist across methods; these differences have not yet been resolved; research to reduce uncertainties and reconcile these differences is underway. Sectorally- and spatially-resolved flux estimates, and detection of changes of fluxes over time, are also active research topics. Major challenges include developing methods for distinguishing anthropogenic from biogenic CO₂ fluxes, improving our ability to interpret atmospheric GHG measurements close to urban GHG sources and across a broader range of atmospheric stability conditions, and quantifying uncertainties in inventory data products. INFLUX data and tools are intended to serve as an open resource and test bed for future investigations. Well-documented, public archival of data and methods is under development in support of this objective.